Mariniflexile maritimum sp. nov., isolated from seawater of the South Sea in the Republic of Korea

A novel Gram-stain-negative, rod-shaped, aerobic, non-motile bacterial strain, designated M5A1M^T, was isolated from seawater collected from the South Sea of the Republic of Korea. Based on 16S rRNA gene sequence similarity, strain M5A1M^T was closely related to Mariniflexile gromovii KMM 6038^T (95.3 %), Mariniflexile fucanivorans SW5^T (95.2 %), Mariniflexile soesokkakense RSSK-9^T (95.1 %), Yeosuana aromativorans GW1-1^T (94.6 %) and Confluentibacter lentus HJM-3^T (94.6 %). Genome-based phylogenetic analyses revealed that strain M5A1M^T formed a distinct cluster with the type strains of the genus Mariniflexile. The major cellular fatty acid constituents (>5 % of the total fatty acids) were iso-C_15:0, anteiso-C_15 : 0, iso-C_15 : 0 3-OH, iso-C_15 : 1 G, iso-C_16:03-OH and iso-C_17 : 0 3-OH. The respiratory quinone was identified as MK-6. The major polar lipids were phosphatidylethanolamine and one unidentified polar lipid. The genomic DNA G+C content of strain M5A1M^T was determined to be 37.7 mol%. On the basis of its phenotypic, phylogenetic and chemotaxonomic characteristics, strain M5A1M^T is considered to represent a novel species within the genus Mariniflexile, for which the name Mariniflexile maritimum sp. nov. is proposed. The type strain is M5A1M^T (=KCTC 72895^T=JCM 33982^T).

Extremophiles in Soil Communities of Former Copper Mining Sites of the East Harz Region (Germany) Reflected by Re-Analyzed 16S rRNA Data

The east and southeast rim of Harz mountains (Germany) are marked by a high density of former copper mining places dating back from the late 20th century to the middle age. A set of 18 soil samples from pre- and early industrial mining places and one sample from an industrial mine dump have been selected for investigation by 16S rRNA and compared with six samples from non-mining areas. Although most of the soil samples from the old mines show pH values around 7, RNA profiling reflects many operational taxonomical units (OTUs) belonging to acidophilic genera. For some of these OTUs, similarities were found with their abundances in the comparative samples, while others show significant differences. In addition to pH-dependent bacteria, thermophilic, psychrophilic, and halophilic types were observed. Among these OTUs, several DNA sequences are related to bacteria which are reported to show the ability to metabolize special substrates. Some OTUs absent in comparative samples from limestone substrates, among them Thaumarchaeota were present in the soil group from ancient mines with pH > 7. In contrast, acidophilic types have been found in a sample from a copper slag deposit, e.g., the polymer degrading bacterium Granulicella and Acidicaldus, which is thermophilic, too. Soil samples of the group of pre-industrial mines supplied some less abundant, interesting OTUs as the polymer-degrading Povalibacter and the halophilic Lewinella and Halobacteriovorax. A particularly high number of bacteria (OTUs) which had not been detected in other samples were found at an industrial copper mine dump, among them many halophilic and psychrophilic types. In summary, the results show that soil samples from the ancient copper mining places contain soil bacterial communities that could be a promising source in the search for microorganisms with valuable metabolic capabilities.

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.

Confluentibacter sediminis sp. nov., isolated from the junction between the ocean and a freshwater lake and emended description of the genus Confluentibacter

A novel marine Gram-stain-negative, non-motile, aerobic and rod-shaped bacterium, designated strain DSL-48^T, was isolated from tidal flat sediment sampled from the East China Sea and characterized phylogenetically and phenotypically. Bacterial optimal growth occurred at 35 °C (range, 4-37 °C), pH 6 (pH 5-10) and with 4 % (w/v) NaCl (0-7 %). The nearest phylogenetic neighbour was Confluentibacter citreus KCTC 52638^T with 16S rRNA gene similarity of 97.1 %. The predominant respiratory quinone was menaquinone-6 (MK-6). The major polar lipids were phosphatidylethanolamine, three unidentified aminolipids and four unidentified lipids. The major fatty acids of strain DSL-48^T were iso-C_15 : 0, iso-C_17 : 0 3-OH, anteiso-C_15 : 0, iso-C_15 : 0 3-OH and iso-C_16 : 0 3-OH. The G+C content of the genomic DNA was 33.3 mol%. The combined genotypic and phenotypic data indicated that strain DSL-48^T represents a novel species of the genus Confluentibacter, for which the name Confluentibacter sediminis sp. nov. is proposed, with the type strain DSL-48^T (=KCTC 62648^T=MCCC 1K03537^T).

Confluentibacter flavum sp. nov., Isolated from the Saline Lake

A Gram-stain-negative, rod-shaped, non-motile, bacterial isolate designated 3B^T, was isolated from a saline lake, and subjected to a polyphasic taxonomic investigation. The phylogenetic analysis based on 16S rRNA gene sequence clearly showed an allocation to the genus Confluentibacter with similarity ranging from 95.1 to 98%. OrthoANI values between strain 3B^T and related strains of Confluentibacter (< 90%) were lower than the threshold value of 95% ANI relatedness recommended for species demarcation. Strain 3B^T grew at 4-35 °C and pH 6.0-8.0 (optimum, 28 °C and pH 6.5) and with 0-3% (w/v) NaCl (optimum, 0.5%). The predominant respiratory quinone was menaquinone-6 (MK-6) and the major fatty acids were iso-C_15:0, iso-C_15:1 G, iso-C_15:0 3-OH, and iso-C_17:0 3-OH. The polar lipid profile of strain 3B^T comprised phosphatidylethanolamine, one unidentified aminolipid, one aminophospholipid, and three unidentified lipids (L1-3). The DNA G+C content was 33.1 mol%. On the basis of morphological, physiological, and chemotaxonomic characteristics, together with the results of phylogenetic analysis, strain 3B^T is described as a novel species in genus Confluentibacter, for which the name Confluentibacter flavum sp. nov. (type strain 3B^T = CGMCC115960^T = KCTC52969^T) is proposed.